The Asian team dominated the early stages, and could have taken the lead through Kensuke Nagai, but his header went just wide. Nagai did break the deadlock minutes later, however, when he rounded the keeper before slotting home.
Egypt were dealt another blow towards the end of the first half as they were reduced to 10 men, Saadeldin Saad the man dismissed for a professional foul.
The second half was an end-to-end affair as both sides looked to get an all-important second goal. It eventually came for Japan with just over 10 minutes left as Maya Yoshida headed home Kiyotake's cross.
The game was finally put beyond all doubt with Japan's third, this time coming courtesy of Otsu who nodded in from close range.
Japan will face the winner of the next quarter-final between Mexico and Senegal.